Tree graphs of RNA secondary structures and their comparisons
Computers and Biomedical Research
Alignment of Trees - An Alternative to Tree Edit
CPM '94 Proceedings of the 5th Annual Symposium on Combinatorial Pattern Matching
Computing Similarity Between RNA Secondary Structures
INTSYS '98 Proceedings of the IEEE International Joint Symposia on Intelligence and Systems
Local Similarity in RNA Secondary Structures
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
A New Distance for High Level RNA Secondary Structure Comparison
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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A tree similarity algorithm for RNA (ribonucleic acid) secondary structure comparison is presented. The elements (nucleotides and nucleotide-pairs) of an RNA secondary structure are represented as normalized node-weighted trees. We show that our weighted tree representations of RNA secondary structures are informative and useful. Based on this unique representation for RNA secondary structure, we propose a weighted-tree similarity algorithm for computing the similarity between RNA secondary structures. The algorithm is justified by computing similarities among several well-known RNA secondary structures. For a given RNA secondary structure, the proposed algorithm provides a ranked list of RNA structures in a database according to their similarity values with the query RNA. Hence, our algorithm is helpful in predicting the functions and the class of a newly discovered RNA.